Bacterial community structure in maize residue amended soil with contrasting management practices
Introduction
Organic matter in soil is of paramount importance for soil fertility, soil structure, water infiltration and erosion prevention (Powlson et al., 2012). Mineralization of organic material define how much C is sequestered in soil and for how long (Johnson et al., 2007). Additionally, mineralization of organic material renders nutrients, especially nitrogen, available for growing plants (Trindade et al., 2001). In more sustainable agricultural practices, i.e. conservation agriculture compared to conventional agriculture, mineralization of crop residues provides crops with a part of their required nutrients (Tejada et al., 2009).
Traditional agricultural practices in Mexico remove crop residue, use heavy tillage and monoculture of maize (Fuentes et al., 2009). Deterioration of soil and a drop in soil fertility as a result of traditional agriculture lead to the development of conservation agriculture that is based on three main principles, such as viable crop rotations, minimum tillage and retention of crop residue in the field (Govaerts et al., 2009). Since 1991, the ‘International Maize and Wheat Improvement Centre’ (CIMMYT) realizes experiments to compare the traditional agricultural practices with conservation agriculture (Govaerts et al., 2009).
In agricultural systems in large parts of the world, especially in Mexico, maize is the main cultivated crop (Mercer and Wainwright, 2008). In rainfed conditions maize is commonly planted on the flat. Raised bed cultivation is frequently used to irrigate crops in semi-arid and arid regions (Sayre, 2004). In most cases the traditional application of raised bed cultivation systems has involved considerable tillage operations to make the beds before planting the next crop and burning of crop residues or using straw for fodder (Aquino, 1998). A next step to increase sustainability is to reduce tillage and manage crop residues on the surface, reusing permanent raised beds with only superficial reshaping in the furrows between the raised beds as needed before planting of each succeeding crop, following even distribution of the previous crop residues (Sayre, 2004). Cultivating crops on beds makes better use of water. Runoff is reduced and water logging of the roots is avoided during the rainy season (Kuotsu et al., 2014). Additionally, operating and energetic costs are reduced with similar or better yields than crops cultivated on the flat (Devkota et al., 2013).
Crop residue contains generally large amounts of (hemi) cellulose so its mineralization will define mostly the residence time of the maize residue in soil and the timing of the release of crop nutrients (Abiven et al., 2005). A complex interaction of microorganisms, mostly bacteria and fungi, metabolizes the crop residue, but little is still known about the organisms involved in their degradation (McGuire and Treseder, 2010). Molecular techniques, such as 454 pyrosequencing of the 16S rRNA gene, allow to study the bacterial and archaeal population in more detail and determine those that are affected by the application of crop residues (Souza et al., 2013).
In a previous study, it was found that agricultural practices affected the bacterial community structure (Navarro-Noya et al., 2013). The relative abundance of Actinobacteria, Betaproteobacteria and Gemmatimonadetes was higher in the tilled than in the untilled soil while that of the Bacteroidetes, Deltaproteobacteria and Verrucomicrobia was lower. When no tillage was applied, crop residue management affected the microbial communities more than when conventional tillage was applied. Wheat–maize rotation or crop monoculture did not affect the bacterial community structure. It remained to be investigated if these differences in bacterial community structure due to different agricultural practices, would alter the bacterial groups involved in the degradation of added organic material. Therefore, the neutral detergent fibre (NDF) fraction of maize residue (Van Soest, 1963, Van Soest and Wine, 1967) or complete maize plants were added to soil. Soil was sampled from four contrasting agricultural practices, i.e. conventional practice and conservation agriculture on the flat or on conventional beds and permanent beds. The bacterial community structure and emissions of CO2 were monitored in an aerobic incubation for 14 days. The objectives of this study were to determine (i) how cultivation practices (conservation agriculture versus conventional practices) affected the bacterial community structure in soil, and (ii) how the bacterial community structure was affected by the application of organic material (NDF or maize residue).
Section snippets
Experimental site
The experimental site is located at El Batán (Texcoco, State of Mexico) in the subtropical highlands of Central Mexico (2240 masl; 19.31°N, 98.50°W) (Govaerts et al., 2008). The mean maximum and minimum temperatures at the experimental site are 24 °C and 6 °C, respectively (1991–2009) and the average annual rainfall is 625 mm year−1, with approximately 545 mm falling between May and October. Short, intense rain showers followed by dry spells typify the summer rainy season and the total yearly
Soil characteristics
In soil cultivated with crops on the flat, the organic C in the CA treatment was significantly higher than in the CP treatment (n = 2, P < 0.05) (Table 2). The other soil characteristics were not significantly different between the CA and CP treatment. In soil cultivated with crops on beds, the organic C and WHC in the PB treatment were significantly higher than in the CB treatment (n = 2, P < 0.05), but the other soil characteristics were not significantly different. The pH was significantly higher in
The relative abundance of bacterial groups in the unamended soil
The relative abundance of phyla that are favoured generally by nutrient depleted environments (e.g. Acidobacteria, Planctomycetes and Verrucomicrobia) was higher in soil with maize cultivated according to conservation agriculture practices than in soil cultivated with maize under conventional practice. Mature compost was found to be a preferred environment for Planctomycetes (de Gannes et al., 2013), while Acidobacteria have frequently be associated with a low nutrient availability and are
Conclusion
Conservation agriculture favours oligotrophic bacteria, e.g. Acidobacteria, Planctomycetes and Verrucomicrobia. In conservation agriculture crop residue remains on the soil surface and it is only through macrofauna activity and leaching that organic material enters the soil. Consequently, little easily decomposable organic material is available for the soil micro-organisms. In conventional practices, the soil is mixed and organic material is brought in direct contact with soil microorganisms so
Acknowledgements
This research was funded by Cinvestav, ‘Apoyo Especial para Fortalecimiento de Doctorado PNPC 2013’ and project ‘Infraestructura 205945’ from ‘Consejo Nacional de Ciencia y Tecnología’ (CONACyT, Mexico), and ‘Centro Internacional de Mejoramiento de Maíz y Trigo’ (CIMMYT) via CRP MAIZE. The research forms part of the strategic research for ‘Desarrollo sustentable con el productor’, part of ‘Modernización Sustentable de la Agricultura Tradicional’, supported by SAGARPA. J.M. B.-L. received a
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Both authors contributed equally to the manuscript.